I beleive you can scale then size of the craft panel

I know you can minimize the craft panel so only the progress bar shows while crafting by simply clicking a box in the craft panel.

I also believe you can scale the size of the panel by placing your cursor at any edge of the panel and dragging to your desired size. (CAVEAT: I say "believe" because I'm not in game to test this ATM.)

Chances are that if the size of multiple panels, not just the crafting panel, that it's most likely because your game resolution is lower than it was before, or your custom UI increases the size. The only one I can remember them increasing themselves was the crafting panel (which you mentioned) but that was quite a while ago.

If it's not resolution or custom UI, maybe look into a custom UI that will shrink them.